Evidence map›Paper›PMID 34230497›Full record

ArticleNature communications2021

Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins.

Zhiwen Liu, Fanglong Zhao, Boyang Zhao, Jie Yang, Joseph Ferrara, Banumathi Sankaran, B V Venkataram Prasad, Biki Bapi Kundu, George N Phillips, Yang Gao and 3 more

Abstract read
In one paragraph

Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.

0numbers the graph read from it
0cells of the map it votes in
21citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

21 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Genome Mining of Isoindolinone-Containing Peptide Natural Products.Journal of the American Chemical Society · 2025
    Article
  5. Review
  6. Article
  7. Article
  8. Article
  9. Review
  10. Biocatalytic Stereoselective Oxidation of 2-Arylindoles.Journal of the American Chemical Society · 2024
    Article
  11. Article
  12. Fungal P450 Deconstructs the 2,5-Diazabicyclo[2.2.2]octane RingJournal of the American Chemical Society · 2023
    Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Unraveling the biosynthesis of penicillenols by genome mining PKS-NRPS gene clusters inAIChE journal. American Institute of Chemical Engineers · 2022
    Article
  18. Article
  19. Article
  20. Rational design of allosteric switchable catalysts.Exploration (Beijing, China) · 2022
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Zhiwen Liu *Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
Fanglong Zhao *Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
Boyang Zhao *Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
Jie YangDepartment of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
Joseph FerraraRigaku Americas Corporation, The Woodlands, TX, USA.ORCID 0000-0001-8534-642X
Banumathi SankaranDepartment of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
B V Venkataram PrasadDepartment of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.ORCID 0000-0002-1172-2071
Biki Bapi KunduPhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA.ORCID 0000-0002-2550-4585
George N PhillipsDepartment of Biosciences, Rice University, Houston, TX, USA.ORCID 0000-0002-4171-4603
Yang GaoDepartment of Biosciences, Rice University, Houston, TX, USA.
Liya HuVerna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.ORCID 0000-0002-8340-8911
Tong ZhuShanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China. tzhu@lps.ecnu.edu.cn.ORCID 0000-0001-7472-3736
Xue GaoDepartment of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA. xue.gao@rice.edu.ORCID 0000-0003-3213-9704

Funding

User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PAUL David ADAMS, Gregory L Hura · 2017 to 2026
$28.6M
Undergraduate Summer Research ExperienceR35GM138207 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI Xue Gao · 2020 to 2026
$2.4M
Natural product-based modulators of 4E-BP1 phosphorylationR01CA203257 · NCI · UNIVERSITY OF KENTUCKY · PI SHE, QING-BAI, THORSON, JON SCOTT · 2016 to 2020
$1.9M
NCI NIH HHS R01 CA203257NIGMS NIH HHS P30 GM124169NIGMS NIH HHS R35 GM138207
6 · The paper itself

Abstract

Prenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.

Indexed as

Biosynthetic PathwaysCatalysisChemistry Techniques, SyntheticCyclohexenesEpoxy CompoundsFermentationFungal ProteinsIndole AlkaloidsModels, MolecularMolecular StructureOxygenasesPenicilliumCyclohexenesEpoxy CompoundsFungal ProteinsIndole AlkaloidsOxygenasessemipinacol

Identifiers

PMID34230497
PMCPMC8260726

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.